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<a href="#pub-methods">Public Member Functions</a> &#124;
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<p>The <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> class creates macromolecule sequence alignments and structure alignments.  
 <a href="classmoltk_1_1Aligner.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="Aligner_8hpp_source.html">Aligner.hpp</a>&gt;</code></p>
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Collaboration diagram for moltk::Aligner:</div>
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<area shape="rect" id="node2" href="classmoltk_1_1MatrixScorer__.html" title="moltk::MatrixScorer_\&lt; moltk::units::Information, 1 \&gt;" alt="" coords="878,37,1199,64"/><area shape="rect" id="node4" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;." alt="" coords="391,12,588,39"/><area shape="rect" id="node8" href="classmoltk_1_1SubstitutionMatrix__.html" title="moltk::SubstitutionMatrix_\&lt; moltk::units::Information \&gt;" alt="" coords="321,63,658,89"/></map>
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<p><a href="classmoltk_1_1Aligner-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a99008604e446e2adc4f0df7e4afd6c9e">Aligner</a> ()</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Construct an <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> with default parameters and no Alignments yet.  <a href="#a99008604e446e2adc4f0df7e4afd6c9e"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align</a> (const <a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> &amp;, const <a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> &amp;)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a92f546677ff4bd7349fe45ee108a3149">get_scorer</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">scorer computes alignment scores.  <a href="#a92f546677ff4bd7349fe45ee108a3149"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#ac60b7a16b4d99c7af16bfcfb9989dc00">get_scorer</a> ()</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">MatrixScorer object this <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> uses to score alignments.  <a href="#ac60b7a16b4d99c7af16bfcfb9989dc00"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Aligner.html">Aligner</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#afac71af10ee7a0436853ae03b38f02dc">set_scorer</a> (const <a class="el" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a> &amp;<a class="el" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">scorer</a>)</td></tr>
<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classmoltk_1_1Aligner.html">Aligner</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a2a94cf962985576ec14640ee519fa371">get_shared_aligner</a> ()</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Global shared aligner object used by <a class="el" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align()</a> method.  <a href="#a2a94cf962985576ec14640ee519fa371"></a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pub-attribs"></a>
Public Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">dp::DPTable<br class="typebreak"/>
&lt; <a class="el" href="namespacemoltk_1_1units.html#a84d2541f1ab08c8ae38bea32fa7b33ca">moltk::units::Information</a>, <br class="typebreak"/>
dp::DP_MEMORY_LARGE, <br class="typebreak"/>
dp::DP_ALIGN_UNGAPPED_SEQUENCES, 1 &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a683da4069fec5bc5b2766792b8f37c04">test_table</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">The actual dynamic programming table.  <a href="#a683da4069fec5bc5b2766792b8f37c04"></a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">scorer</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>The <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> class creates macromolecule sequence alignments and structure alignments. </p>
</div><hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="a99008604e446e2adc4f0df7e4afd6c9e"></a><!-- doxytag: member="moltk::Aligner::Aligner" ref="a99008604e446e2adc4f0df7e4afd6c9e" args="()" -->
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          <td class="memname">moltk::Aligner::Aligner </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Construct an <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> with default parameters and no Alignments yet. </p>

</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a12bd197b84d50d7c1e8f952c91eb7666"></a><!-- doxytag: member="moltk::Aligner::align" ref="a12bd197b84d50d7c1e8f952c91eb7666" args="(const Alignment &amp;, const Alignment &amp;)" -->
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          <td class="memname"><a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> moltk::Aligner::align </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> &amp;&#160;</td>
          <td class="paramname">, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> &amp;&#160;</td>
          <td class="paramname">&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td></td>
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<div class="memdoc">

</div>
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<a class="anchor" id="a92f546677ff4bd7349fe45ee108a3149"></a><!-- doxytag: member="moltk::Aligner::get_scorer" ref="a92f546677ff4bd7349fe45ee108a3149" args="() const " -->
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          <td class="memname">const <a class="el" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a>&amp; moltk::Aligner::get_scorer </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
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<div class="memdoc">

<p>scorer computes alignment scores. </p>

</div>
</div>
<a class="anchor" id="ac60b7a16b4d99c7af16bfcfb9989dc00"></a><!-- doxytag: member="moltk::Aligner::get_scorer" ref="ac60b7a16b4d99c7af16bfcfb9989dc00" args="()" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname"><a class="el" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a>&amp; moltk::Aligner::get_scorer </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [inline]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>MatrixScorer object this <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> uses to score alignments. </p>

</div>
</div>
<a class="anchor" id="a2a94cf962985576ec14640ee519fa371"></a><!-- doxytag: member="moltk::Aligner::get_shared_aligner" ref="a2a94cf962985576ec14640ee519fa371" args="()" -->
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<div class="memproto">
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        <tr>
          <td class="memname">static <a class="el" href="classmoltk_1_1Aligner.html">Aligner</a>&amp; moltk::Aligner::get_shared_aligner </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [static]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Global shared aligner object used by <a class="el" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align()</a> method. </p>

</div>
</div>
<a class="anchor" id="afac71af10ee7a0436853ae03b38f02dc"></a><!-- doxytag: member="moltk::Aligner::set_scorer" ref="afac71af10ee7a0436853ae03b38f02dc" args="(const MatrixScorer &amp;scorer)" -->
<div class="memitem">
<div class="memproto">
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          <td class="memname"><a class="el" href="classmoltk_1_1Aligner.html">Aligner</a>&amp; moltk::Aligner::set_scorer </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a> &amp;&#160;</td>
          <td class="paramname"><em>scorer</em></td><td>)</td>
          <td><code> [inline]</code></td>
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<div class="memdoc">

</div>
</div>
<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="ae5864cedf09cec9ea5e8ea5967f505c9"></a><!-- doxytag: member="moltk::Aligner::scorer" ref="ae5864cedf09cec9ea5e8ea5967f505c9" args="" -->
<div class="memitem">
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      <table class="memname">
        <tr>
          <td class="memname"><a class="el" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a> <a class="el" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">moltk::Aligner::scorer</a><code> [protected]</code></td>
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<div class="memdoc">

</div>
</div>
<a class="anchor" id="a683da4069fec5bc5b2766792b8f37c04"></a><!-- doxytag: member="moltk::Aligner::test_table" ref="a683da4069fec5bc5b2766792b8f37c04" args="" -->
<div class="memitem">
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        <tr>
          <td class="memname">dp::DPTable&lt;<a class="el" href="namespacemoltk_1_1units.html#a84d2541f1ab08c8ae38bea32fa7b33ca">moltk::units::Information</a>, dp::DP_MEMORY_LARGE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, 1&gt; <a class="el" href="classmoltk_1_1Aligner.html#a683da4069fec5bc5b2766792b8f37c04">moltk::Aligner::test_table</a></td>
        </tr>
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<div class="memdoc">

<p>The actual dynamic programming table. </p>

</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="Aligner_8hpp_source.html">Aligner.hpp</a></li>
</ul>
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